Here is what happened and why it was not included in Crysis 2.
Nomad and Psycho were fighting on opposite sides of the island. So After C1 Nomad went back in to destroy the alien mothership. And Psycho, well he did the same.
They bumped into each other on their way there. As you are aware it was extremely cold with everything being frozed. So they huddles up overnight, getting ready to attack at first light. While spending the night they started feeling very strange. Something they have never felt before.
Yes, they fell in love with each other. A passionate Nano love session insued and lasted the entire night. After this they started thinking they could not bare to live without one another, and switched to cloak mode and sneaked off to a neighbouring island. They did not want to risk losing each other.
Prophet got word of this, and followed them. After seeing them together he was suddenly overwhelmed by emotions he could not explain. He joined in, and they all got STD's.
The STD's is why you see Prophet furious is Crysis 2, yelling some garble about they new that the nano suit will not protect them against STD's, and now they are all walking dead. You see the goverment lied. They said it will protect against everything. Obviously it does against bullets and aliens and extreme conditions. But the Goverment failed to take orgies into account.
EA then had to cut this from the story because they knew some underage kids will get their hands on the game. Also they did not want to up their rating to accomodate the sixual scenes.
Well there you have it.